Structure

Physi-Chem Properties

Molecular Weight:  165.05
Volume:  148.276
LogP:  -3.078
LogD:  -1.961
LogS:  -0.611
# Rotatable Bonds:  4
TPSA:  86.38
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.532
Synthetic Accessibility Score:  4.414
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.822
MDCK Permeability:  0.0007366936188191175
Pgp-inhibitor:  0.001
Pgp-substrate:  0.966
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.036
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.383
Plasma Protein Binding (PPB):  7.915317535400391%
Volume Distribution (VD):  0.51
Pgp-substrate:  90.43307495117188%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.058
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.06
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.398
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.201
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.026

ADMET: Excretion

Clearance (CL):  5.245
Half-life (T1/2):  0.653

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.18
Drug-inuced Liver Injury (DILI):  0.026
AMES Toxicity:  0.259
Rat Oral Acute Toxicity:  0.067
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.149
Carcinogencity:  0.921
Eye Corrosion:  0.008
Eye Irritation:  0.054
Respiratory Toxicity:  0.134

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC317815

Natural Product ID:  NPC317815
Common Name*:   Methionine Sulfoxide
IUPAC Name:   (2S)-2-amino-4-methylsulfinylbutanoic acid
Synonyms:  
Standard InCHIKey:  QEFRNWWLZKMPFJ-YGVKFDHGSA-N
Standard InCHI:  InChI=1S/C5H11NO3S/c1-10(9)3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-,10?/m0/s1
SMILES:  CS(=O)CCC(C(=O)[O-])[NH3+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL445753
PubChem CID:   158980
1548907
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002404] Alpha amino acids
                • [CHEMONTID:0004146] L-alpha-amino acids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1016/0006-291X(79)91731-5]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1093/emboj/18.8.2021]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1091286]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[10977898]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1100617]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11745165]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11750815]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12369847]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12467448]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12805358]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. ChEBI[131529]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13610867]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13831814]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[14973046]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15031653]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15292242]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15610037]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1644759]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[16630633]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[170247]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[17765195]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[179975]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19026742]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19514719]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19561621]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21437340]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21988831]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22289691]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22855027]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23537328]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23676670]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[241475]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24206068]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24783849]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24831709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24939187]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24966042]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24967680]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[2543976]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[25867074]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26195826]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26337258]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26670289]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26826371]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29897754]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30302998]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[318639]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[3283102]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[398096]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4877125]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4879561]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4908789]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[5332408]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6102982]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6284709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6338507]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7042909]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7601837]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[8852895]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[9470222]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT4187 Individual Protein Gamma-glutamyltranspeptidase 1 Rattus norvegicus Ki = 5900000.0 nM PMID[447865]
NPT2 Others Unspecified Inhibition = 11.0 % PMID[447866]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC317815 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.96 High Similarity NPC102815
0.9375 High Similarity NPC193989
0.9375 High Similarity NPC170739
0.9375 High Similarity NPC152451
0.8958 High Similarity NPC204364
0.875 High Similarity NPC198196
0.8367 Intermediate Similarity NPC49952
0.8367 Intermediate Similarity NPC136476
0.8182 Intermediate Similarity NPC82239
0.8077 Intermediate Similarity NPC114990
0.7843 Intermediate Similarity NPC118187
0.7759 Intermediate Similarity NPC321419
0.7736 Intermediate Similarity NPC125736
0.7708 Intermediate Similarity NPC326992
0.7708 Intermediate Similarity NPC121517
0.7708 Intermediate Similarity NPC168375
0.7692 Intermediate Similarity NPC318523
0.7647 Intermediate Similarity NPC185755
0.7647 Intermediate Similarity NPC213876
0.7636 Intermediate Similarity NPC145235
0.7551 Intermediate Similarity NPC254482
0.7551 Intermediate Similarity NPC110533
0.7551 Intermediate Similarity NPC326808
0.7551 Intermediate Similarity NPC317691
0.74 Intermediate Similarity NPC291186
0.74 Intermediate Similarity NPC167986
0.7255 Intermediate Similarity NPC325097
0.7255 Intermediate Similarity NPC132307
0.7255 Intermediate Similarity NPC126925
0.7241 Intermediate Similarity NPC283786
0.7115 Intermediate Similarity NPC118459
0.7115 Intermediate Similarity NPC327698
0.7115 Intermediate Similarity NPC191136
0.7 Intermediate Similarity NPC53449
0.7 Intermediate Similarity NPC66043
0.6981 Remote Similarity NPC228932
0.6875 Remote Similarity NPC116709
0.6875 Remote Similarity NPC21290
0.6875 Remote Similarity NPC272614
0.6792 Remote Similarity NPC329263
0.6786 Remote Similarity NPC319175
0.6667 Remote Similarity NPC248970
0.6667 Remote Similarity NPC306238
0.6607 Remote Similarity NPC245027
0.6607 Remote Similarity NPC43204
0.6607 Remote Similarity NPC84636
0.6607 Remote Similarity NPC62045
0.6607 Remote Similarity NPC162620
0.6607 Remote Similarity NPC174246
0.6607 Remote Similarity NPC93888
0.6607 Remote Similarity NPC226027
0.6607 Remote Similarity NPC270805
0.6604 Remote Similarity NPC198301
0.6545 Remote Similarity NPC136159
0.6491 Remote Similarity NPC315977
0.6481 Remote Similarity NPC285322
0.6481 Remote Similarity NPC208793
0.6429 Remote Similarity NPC153370
0.6429 Remote Similarity NPC93081
0.6429 Remote Similarity NPC140872
0.64 Remote Similarity NPC63621
0.6364 Remote Similarity NPC309658
0.6364 Remote Similarity NPC297220
0.6346 Remote Similarity NPC326212
0.6346 Remote Similarity NPC237525
0.6316 Remote Similarity NPC328378
0.6316 Remote Similarity NPC316231
0.6316 Remote Similarity NPC324825
0.6316 Remote Similarity NPC112890
0.6308 Remote Similarity NPC289691
0.6275 Remote Similarity NPC18188
0.625 Remote Similarity NPC14778
0.6212 Remote Similarity NPC174304
0.6212 Remote Similarity NPC325597
0.6207 Remote Similarity NPC273330
0.6207 Remote Similarity NPC137958
0.62 Remote Similarity NPC9294
0.6167 Remote Similarity NPC321118
0.6167 Remote Similarity NPC316889
0.6154 Remote Similarity NPC329545
0.6066 Remote Similarity NPC2801
0.6 Remote Similarity NPC190184
0.6 Remote Similarity NPC197087
0.5968 Remote Similarity NPC38463
0.5965 Remote Similarity NPC181588
0.5942 Remote Similarity NPC319046
0.5926 Remote Similarity NPC226265
0.5926 Remote Similarity NPC219143
0.5902 Remote Similarity NPC60672
0.5902 Remote Similarity NPC183845
0.5902 Remote Similarity NPC322091
0.5902 Remote Similarity NPC279661
0.5873 Remote Similarity NPC278209
0.5857 Remote Similarity NPC126779
0.5833 Remote Similarity NPC155156
0.5833 Remote Similarity NPC200550
0.5833 Remote Similarity NPC315897
0.5818 Remote Similarity NPC276294
0.5806 Remote Similarity NPC327831
0.5781 Remote Similarity NPC190385
0.5781 Remote Similarity NPC176164
0.5781 Remote Similarity NPC189301
0.5714 Remote Similarity NPC323974
0.5714 Remote Similarity NPC325985
0.5692 Remote Similarity NPC254541
0.5692 Remote Similarity NPC327748
0.5692 Remote Similarity NPC316826
0.5692 Remote Similarity NPC317143
0.5692 Remote Similarity NPC321468
0.5625 Remote Similarity NPC317147
0.5625 Remote Similarity NPC318260
0.5606 Remote Similarity NPC329564
0.5606 Remote Similarity NPC327170
0.56 Remote Similarity NPC114517

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC317815 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.9375 High Similarity NPD8803 Clinical (unspecified phase)
0.9375 High Similarity NPD8802 Approved
0.9375 High Similarity NPD9021 Approved
0.875 High Similarity NPD9020 Approved
0.8462 Intermediate Similarity NPD8849 Clinical (unspecified phase)
0.84 Intermediate Similarity NPD8873 Approved
0.8077 Intermediate Similarity NPD9025 Approved
0.7647 Intermediate Similarity NPD8982 Approved
0.7647 Intermediate Similarity NPD8801 Approved
0.7551 Intermediate Similarity NPD8214 Approved
0.7551 Intermediate Similarity NPD8215 Approved
0.74 Intermediate Similarity NPD8804 Approved
0.74 Intermediate Similarity NPD8805 Approved
0.7255 Intermediate Similarity NPD8798 Approved
0.6923 Remote Similarity NPD9452 Clinical (unspecified phase)
0.6875 Remote Similarity NPD8211 Approved
0.6875 Remote Similarity NPD8210 Phase 3
0.6833 Remote Similarity NPD8848 Approved
0.6727 Remote Similarity NPD8577 Discontinued
0.6667 Remote Similarity NPD8870 Approved
0.6618 Remote Similarity NPD2262 Clinical (unspecified phase)
0.6607 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6607 Remote Similarity NPD9018 Approved
0.6607 Remote Similarity NPD8624 Approved
0.6607 Remote Similarity NPD9017 Approved
0.6481 Remote Similarity NPD8610 Approved
0.6429 Remote Similarity NPD8809 Approved
0.6429 Remote Similarity NPD8614 Approved
0.6429 Remote Similarity NPD9214 Phase 3
0.6429 Remote Similarity NPD9213 Approved
0.6429 Remote Similarity NPD8808 Approved
0.6316 Remote Similarity NPD9044 Approved
0.6275 Remote Similarity NPD8623 Phase 1
0.6271 Remote Similarity NPD9386 Approved
0.6269 Remote Similarity NPD886 Clinical (unspecified phase)
0.6212 Remote Similarity NPD348 Approved
0.6207 Remote Similarity NPD8872 Phase 3
0.6207 Remote Similarity NPD8871 Approved
0.6207 Remote Similarity NPD329 Discontinued
0.6 Remote Similarity NPD8785 Approved
0.6 Remote Similarity NPD8869 Approved
0.6 Remote Similarity NPD9420 Clinical (unspecified phase)
0.6 Remote Similarity NPD8851 Phase 1
0.5965 Remote Similarity NPD8810 Clinical (unspecified phase)
0.5946 Remote Similarity NPD9389 Approved
0.5942 Remote Similarity NPD337 Discontinued
0.5942 Remote Similarity NPD4241 Registered
0.5926 Remote Similarity NPD8609 Approved
0.5926 Remote Similarity NPD8217 Clinical (unspecified phase)
0.5926 Remote Similarity NPD8216 Approved
0.5857 Remote Similarity NPD4242 Approved
0.5833 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5781 Remote Similarity NPD9433 Approved
0.5781 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9019 Approved
0.5696 Remote Similarity NPD7643 Phase 1
0.5606 Remote Similarity NPD902 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data